pre-miRNA Information
pre-miRNA hsa-mir-873   
Genomic Coordinates chr9: 28888879 - 28888955
Synonyms MIRN873, hsa-mir-873, MIR873
Description Homo sapiens miR-873 stem-loop
Comment This sequence was identified as a miRNA candidate by Berezikov et al. using RAKE and MPSS techniques .
RNA Secondary Structure
Associated Diseases

Mature miRNA Information
Mature miRNA hsa-miR-873-3p
Sequence 46| GGAGACUGAUGAGUUCCCGGGA |67
Evidence Not_experimental
Experiments
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs760528397 3 dbSNP
rs773403294 9 dbSNP
rs1273846238 13 dbSNP
rs1339396073 15 dbSNP
rs1247999695 18 dbSNP
rs377380148 19 dbSNP
Putative Targets

miRNA Expression profile
Human miRNA Tissue Atlas
miRNAs in Extracellular Vesicles
Circulating MicroRNA Expression Profiling
Gene Information
Gene Symbol ZNF549   
Synonyms -
Description zinc finger protein 549
Transcript NM_153263   
Expression
Putative miRNA Targets on ZNF549
3'UTR of ZNF549
(miRNA target sites are highlighted)
>ZNF549|NM_153263|3'UTR
   1 CAATTGTTGGGATGTGTAATTGTCTTATTCACTGTAGGACACCAGAGAGCTGATTTTTCAAGGGATCCAACAGACAGAAA
  81 TTCACCCTCATACATCTGCATATCACTAGTTGAAAGATTCACTACAAGGTCCAAGTACTTGGGAAGCTTTCTAGAGATTA
 161 CTTGTACTTTCTAATCTGCCCAGTGTTACAACAGACACTACCATGTGGCATATCCTCACCGTTTTCATCAGTCACTCACA
 241 TGTGCTCAAGGAATGCAGACCACTGTGCTTACCAAATTCTGAAGGGAATAATATAATAAAAGCCTGTTGAGGGTCCTCTT
 321 CCATCTTGCTGAACTGTTCGAGGCAAAGACAAAACCCAACTTTGACCAAGAAGAGCAATCTGGATTCTTGTAGCCCATGG
 401 AGGTTTACCTTCTTCATAGGTTTTTTTTTTTTTTATGTGATTGCCATAGTGGGATATTCCCTCTCCCACATTACCCAAGA
 481 GGGAAATGGGCTGTCTTACCATGTGCTGATGTATGTGCTCTGCCAGTGTGAAGGGTGAACAGCTCCAACTTTATGTCCCC
 561 CCAGGGACATAGTATGAGATCGGAAAATAGTTCTTAGTCCTGTTTGTCTTAATTTTTATTGGTTTCCAAGGTCTCCTAGG
 641 AAGGAGAGCAGAGCTGTGTGGTCCTAATCATGGTGTCGATGCCAGATTTATTTGTAGGTCCAGAGGTCTCCCTGAGAAGA
 721 GGCATTTGTGACAAACTCAAGTGCTGGGACCTGCATGAATTGTTTATTTGCAGTGATGCTTCATATTTCCCAGCACTGTT
 801 CATGGTATCTTATTTCCCAGGTCCTTCATTGTAGCCATGGGCACTGAAGGACTGAATTGGTAGGTAGGTCACTGGTTGTA
 881 AGACCTACTGGGGCCAGGTAAGAACAGTAATTGGCCCAGACAGGTAGGTGTGATAAACAGAGTAGAAAAGATTGTGGCCA
 961 AGAAGAGTGAATGTGTCCCATCCAAAGGTGCATCCAGATATGTCTGTGTTACTATGGCTTCATGGTTTGGGGGTATATAG
1041 AAATTCTCAGGACCTCAGACCTTTGATTCTCCTTTAGCAACACACATCGTCAGCATAAGGCATCTAAAGATTTTGTGGAC
1121 TCATAACTTATGTACTGTTTTTGAGATGATTGCTGCACGGGCAGGAAAGCAGGATTTGAGAGAACATACACCTTGCCTTC
1201 CAGATATGTGGTTTTTGTGATTCACCCAGATCTGTTGTGCCAGTTAGGAATTATCTTTATTACTTCCCGTTTATTGCCAC
1281 TGCTGAGAAGGCTGTCCTTCCTAACTTGTGAGGAGATGAATCCTTAATAATAAGTAAATCTTGTGTTATCCTATAGTCTG
1361 GTTTTCCAAAAGGAGAGGTAGATGCATATTTTTGTGTGGAACCATTTATCTTAAAACATTGAGGTGCAGTTTTCATACAC
1441 AAAACCTTCTATCTTTTTAAGAACTGTCTGTATGGTTTATTGCCCAGTTAATGGGTTTTGATAGTCATGTTATCTCAGTA
1521 AGTGTCTTGTCTTAGAAATATGTGTGTATAGGCTGGGTGCGGTGGCTCATGCCTGTAATCCCAGCACTTTGGGAGGCCAA
1601 GGCAGGTGGATCACCTGAGGTCAGGAGTTTGAGACCAGCCTGACCAACATGGTGAAATCCAGTCTCTACTTAAAATACAA
1681 AAATTAGCCAGGCGTGGTGGCGTGCATTTGTAATCCCAGCTACACAGGAGGCTGAGGCAGGAGAATTGCTTGAACCTGGG
1761 GGGCGGAGGTTGCAATGAGCCAAGGTCGCGCCATTGCACTCCAGCCTGGGCGACAGAGTGACACTTCTCAAAAAACAAAA
1841 ACAAAAACAAAAAGAACAGATAAGAAATACGTGTGTATATATTCTATTTTGTGTGTTTTCATTCACCTTATTTCATTCAG
1921 TCTTCCAAATGAAATGTTCTTAATTTTGAAAAAAAAAAAAAAAA
Target sites Provided by authors   Predicted by miRanda    DRVs    SNPs    DRVs & SNPs
miRNA-target interactions
(Predicted by miRanda)
ID Duplex structure Position Score MFE
1
miRNA  3' aggGCC-CUUGAGUAGUCAGAGg 5'
             :|| ||| ||  ||||||| 
Target 5' acaTGGTGAAATC--CAGTCTCt 3'
1647 - 1667 155.00 -16.40
2
miRNA  3' agggcccUUGAGU-AGUCAGAGg 5'
                 | :||| |||||||: 
Target 5' tcaccttATTTCATTCAGTCTTc 3'
1903 - 1925 139.00 -17.30
3
miRNA  3' agggcccuuGAGUAGUCAGAGg 5'
                   :||||||||| | 
Target 5' ctcaccgttTTCATCAGTCACt 3'
215 - 236 129.00 -18.70
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN13839508 10 COSMIC
COSN30517674 13 COSMIC
COSN30481976 69 COSMIC
COSN30494710 92 COSMIC
COSN1219367 97 COSMIC
COSN31524290 111 COSMIC
COSN31603081 113 COSMIC
COSN31482966 121 COSMIC
COSN4968480 286 COSMIC
COSN32160503 341 COSMIC
COSN18766363 435 COSMIC
COSN27460731 435 COSMIC
COSN20093669 733 COSMIC
COSN16623967 1160 COSMIC
COSN21582612 1382 COSMIC
COSN1772828 1676 COSMIC
COSN4968481 1716 COSMIC
COSN29944327 1899 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs1303457945 1 dbSNP
rs1217480313 4 dbSNP
rs1340660219 5 dbSNP
rs1327370949 10 dbSNP
rs747375367 15 dbSNP
rs1260829279 22 dbSNP
rs201171961 23 dbSNP
rs752258850 25 dbSNP
rs184207198 26 dbSNP
rs975042695 27 dbSNP
rs763863485 29 dbSNP
rs769048830 30 dbSNP
rs922893296 32 dbSNP
rs1159270280 34 dbSNP
rs1314635253 38 dbSNP
rs1343223756 39 dbSNP
rs757657933 48 dbSNP
rs1455342604 53 dbSNP
rs150273851 56 dbSNP
rs956278220 71 dbSNP
rs1398300623 76 dbSNP
rs990156795 80 dbSNP
rs914610033 84 dbSNP
rs781351196 87 dbSNP
rs1197850210 90 dbSNP
rs1185141266 94 dbSNP
rs562273011 97 dbSNP
rs1477965128 100 dbSNP
rs980374067 105 dbSNP
rs528007292 110 dbSNP
rs373733790 119 dbSNP
rs941850984 120 dbSNP
rs1201385775 125 dbSNP
rs1037524727 129 dbSNP
rs928868662 130 dbSNP
rs1235965960 132 dbSNP
rs1197679904 142 dbSNP
rs1422148646 144 dbSNP
rs1317959883 148 dbSNP
rs367846420 154 dbSNP
rs1216994270 158 dbSNP
rs938877544 159 dbSNP
rs1344150803 160 dbSNP
rs916429866 164 dbSNP
rs748393073 165 dbSNP
rs767208890 168 dbSNP
rs769807706 171 dbSNP
rs947942017 172 dbSNP
rs370991616 173 dbSNP
rs907162278 174 dbSNP
rs1173981917 184 dbSNP
rs929026398 186 dbSNP
rs1002906908 191 dbSNP
rs1426406448 192 dbSNP
rs1258321631 193 dbSNP
rs1053189058 197 dbSNP
rs1324932978 198 dbSNP
rs773347907 204 dbSNP
rs1380119035 214 dbSNP
rs112521311 216 dbSNP
rs1239638306 221 dbSNP
rs559602438 222 dbSNP
rs996798390 235 dbSNP
rs1279224583 239 dbSNP
rs1220920934 243 dbSNP
rs1344819984 245 dbSNP
rs774208153 246 dbSNP
rs759378518 248 dbSNP
rs1290388925 249 dbSNP
rs1240628092 251 dbSNP
rs767439635 255 dbSNP
rs1017532915 256 dbSNP
rs1301320710 258 dbSNP
rs1030616815 262 dbSNP
rs1359869140 281 dbSNP
rs901720131 282 dbSNP
rs954376600 293 dbSNP
rs188492620 299 dbSNP
rs1159572024 303 dbSNP
rs983103944 305 dbSNP
rs997378462 309 dbSNP
rs1179818838 315 dbSNP
rs1312741492 317 dbSNP
rs112813880 319 dbSNP
rs973194374 332 dbSNP
rs1487238061 337 dbSNP
rs532756643 340 dbSNP
rs1216986230 341 dbSNP
rs760405535 357 dbSNP
rs1283021210 360 dbSNP
rs1314734202 361 dbSNP
rs1228003272 367 dbSNP
rs1021714516 368 dbSNP
rs1046734022 370 dbSNP
rs1398248898 378 dbSNP
rs549324566 387 dbSNP
rs927941153 390 dbSNP
rs1242364708 391 dbSNP
rs763718515 396 dbSNP
rs1465601560 397 dbSNP
rs970080017 398 dbSNP
rs111267783 406 dbSNP
rs959850410 408 dbSNP
rs1053081338 409 dbSNP
rs891822240 413 dbSNP
rs947416850 414 dbSNP
rs1414091519 415 dbSNP
rs928904164 417 dbSNP
rs938907635 418 dbSNP
rs1194372420 421 dbSNP
rs1263415094 421 dbSNP
rs1476557523 421 dbSNP
rs571365765 421 dbSNP
rs900660594 423 dbSNP
rs972937311 424 dbSNP
rs1292302138 425 dbSNP
rs918776578 431 dbSNP
rs1216873718 433 dbSNP
rs1279368094 435 dbSNP
rs931481555 435 dbSNP
rs992954797 436 dbSNP
rs1469043940 438 dbSNP
rs1334507201 439 dbSNP
rs1384897612 440 dbSNP
rs1453339846 444 dbSNP
rs753374805 447 dbSNP
rs1370481085 454 dbSNP
rs1350040093 464 dbSNP
rs1166728845 483 dbSNP
rs887496751 503 dbSNP
rs943042115 505 dbSNP
rs1039087446 512 dbSNP
rs1225003232 513 dbSNP
rs1422353455 515 dbSNP
rs1014518571 521 dbSNP
rs1430188501 560 dbSNP
rs756764198 567 dbSNP
rs1265202333 568 dbSNP
rs901773718 569 dbSNP
rs997871434 575 dbSNP
rs1031569844 579 dbSNP
rs891672554 583 dbSNP
rs766878242 588 dbSNP
rs752037530 601 dbSNP
rs796498248 607 dbSNP
rs1261736556 609 dbSNP
rs973527350 610 dbSNP
rs1463028408 624 dbSNP
rs760305815 632 dbSNP
rs1220565249 640 dbSNP
rs1021724359 643 dbSNP
rs1301190530 644 dbSNP
rs1387702979 649 dbSNP
rs796739274 654 dbSNP
rs1232840447 655 dbSNP
rs970089968 657 dbSNP
rs1468606852 671 dbSNP
rs1399121715 674 dbSNP
rs117128606 678 dbSNP
rs1463074382 679 dbSNP
rs1375858927 682 dbSNP
rs1175349101 690 dbSNP
rs1433537861 695 dbSNP
rs1396706948 698 dbSNP
rs772756996 710 dbSNP
rs1469540168 711 dbSNP
rs1457441206 712 dbSNP
rs1239029921 729 dbSNP
rs571561850 733 dbSNP
rs927797214 737 dbSNP
rs1470147330 738 dbSNP
rs1255907798 742 dbSNP
rs548941110 746 dbSNP
rs1234665670 747 dbSNP
rs565256622 749 dbSNP
rs935213707 757 dbSNP
rs973437112 760 dbSNP
rs748305190 762 dbSNP
rs952891566 764 dbSNP
rs988061809 773 dbSNP
rs1309621714 779 dbSNP
rs1392616193 784 dbSNP
rs1328058838 787 dbSNP
rs1399502821 795 dbSNP
rs1302165803 797 dbSNP
rs984216325 802 dbSNP
rs1466446779 804 dbSNP
rs1377218004 814 dbSNP
rs1352696331 827 dbSNP
rs530704374 831 dbSNP
rs913204550 840 dbSNP
rs756325733 841 dbSNP
rs1184318315 842 dbSNP
rs1422110095 846 dbSNP
rs777918814 870 dbSNP
rs1201130710 879 dbSNP
rs1486906645 881 dbSNP
rs749369059 883 dbSNP
rs1038768545 884 dbSNP
rs1279687674 886 dbSNP
rs1216342258 887 dbSNP
rs368301748 899 dbSNP
rs1279751306 904 dbSNP
rs1240799860 907 dbSNP
rs900609326 922 dbSNP
rs1311321169 931 dbSNP
rs1396116767 935 dbSNP
rs1357214470 937 dbSNP
rs1296333118 939 dbSNP
rs932998356 941 dbSNP
rs770960985 953 dbSNP
rs1053479708 954 dbSNP
rs192430331 957 dbSNP
rs1160481404 970 dbSNP
rs1456546577 978 dbSNP
rs1051908475 981 dbSNP
rs1476267270 989 dbSNP
rs1011416856 996 dbSNP
rs1042886355 999 dbSNP
rs890641296 1002 dbSNP
rs1326047317 1003 dbSNP
rs905958079 1005 dbSNP
rs1002052094 1007 dbSNP
rs145674946 1009 dbSNP
rs960352176 1012 dbSNP
rs1206708115 1025 dbSNP
rs1208451248 1029 dbSNP
rs1353745971 1029 dbSNP
rs994549786 1031 dbSNP
rs771922690 1033 dbSNP
rs1252675583 1039 dbSNP
rs994149878 1054 dbSNP
rs1264494212 1057 dbSNP
rs1025856998 1064 dbSNP
rs1023785174 1070 dbSNP
rs952943696 1074 dbSNP
rs1336382949 1079 dbSNP
rs1241754606 1082 dbSNP
rs969193001 1083 dbSNP
rs982288880 1085 dbSNP
rs1034814488 1089 dbSNP
rs956536032 1090 dbSNP
rs988051912 1093 dbSNP
rs1164111845 1100 dbSNP
rs984267274 1111 dbSNP
rs1334459222 1117 dbSNP
rs915204076 1122 dbSNP
rs1197480489 1123 dbSNP
rs182000843 1131 dbSNP
rs911419786 1132 dbSNP
rs964226109 1133 dbSNP
rs1478409379 1138 dbSNP
rs539848259 1142 dbSNP
rs974937424 1143 dbSNP
rs556571620 1151 dbSNP
rs764738932 1153 dbSNP
rs923036952 1156 dbSNP
rs576623425 1159 dbSNP
rs1052730237 1160 dbSNP
rs1217506575 1161 dbSNP
rs1411657316 1170 dbSNP
rs542291816 1186 dbSNP
rs913170078 1187 dbSNP
rs1308082449 1188 dbSNP
rs932059902 1189 dbSNP
rs1330355295 1193 dbSNP
rs1326795220 1201 dbSNP
rs947255685 1205 dbSNP
rs775418192 1208 dbSNP
rs1042979488 1219 dbSNP
rs1051798978 1221 dbSNP
rs1304509343 1226 dbSNP
rs1410605783 1231 dbSNP
rs912024938 1233 dbSNP
rs760601684 1240 dbSNP
rs940893968 1248 dbSNP
rs1001370288 1251 dbSNP
rs1270046233 1252 dbSNP
rs1469493022 1264 dbSNP
rs1057465260 1265 dbSNP
rs1337978589 1268 dbSNP
rs763778518 1269 dbSNP
rs994596238 1285 dbSNP
rs1437966285 1292 dbSNP
rs1275004953 1299 dbSNP
rs994897694 1300 dbSNP
rs1044714344 1310 dbSNP
rs1303815590 1311 dbSNP
rs187266765 1319 dbSNP
rs1236243255 1324 dbSNP
rs1374857948 1328 dbSNP
rs1308884049 1329 dbSNP
rs138357937 1332 dbSNP
rs190850274 1335 dbSNP
rs1452471241 1343 dbSNP
rs776184615 1344 dbSNP
rs1034801656 1346 dbSNP
rs182079260 1347 dbSNP
rs1018478834 1348 dbSNP
rs1376616426 1350 dbSNP
rs1175856701 1352 dbSNP
rs1009429324 1355 dbSNP
rs1378086075 1360 dbSNP
rs964594949 1363 dbSNP
rs1192200796 1371 dbSNP
rs1240184943 1377 dbSNP
rs1177678752 1378 dbSNP
rs976912782 1379 dbSNP
rs1030496777 1383 dbSNP
rs1207445128 1390 dbSNP
rs1441719049 1395 dbSNP
rs1280954129 1399 dbSNP
rs1212744300 1400 dbSNP
rs116349134 1404 dbSNP
rs988487348 1405 dbSNP
rs1285549552 1418 dbSNP
rs1384536363 1419 dbSNP
rs577869013 1420 dbSNP
rs912929645 1427 dbSNP
rs947015147 1436 dbSNP
rs1282451409 1437 dbSNP
rs1447408892 1438 dbSNP
rs1422149286 1439 dbSNP
rs1164992513 1441 dbSNP
rs1315432157 1446 dbSNP
rs149557277 1452 dbSNP
rs562929412 1459 dbSNP
rs1360338210 1472 dbSNP
rs921915007 1488 dbSNP
rs953509156 1491 dbSNP
rs187036559 1494 dbSNP
rs987506424 1496 dbSNP
rs937176004 1500 dbSNP
rs375159057 1507 dbSNP
rs1258117877 1508 dbSNP
rs144257532 1509 dbSNP
rs1487167015 1512 dbSNP
rs1262151743 1513 dbSNP
rs1324998335 1519 dbSNP
rs930105821 1531 dbSNP
rs368021616 1536 dbSNP
rs368522922 1539 dbSNP
rs1005500813 1540 dbSNP
rs904849354 1541 dbSNP
rs1003250304 1542 dbSNP
rs752007328 1547 dbSNP
rs900041942 1552 dbSNP
rs998777713 1555 dbSNP
rs755481222 1561 dbSNP
rs567499524 1562 dbSNP
rs112161597 1567 dbSNP
rs1022115856 1573 dbSNP
rs1260975252 1582 dbSNP
rs1020040443 1594 dbSNP
rs756521883 1596 dbSNP
rs551558423 1602 dbSNP
rs1188984932 1604 dbSNP
rs762326591 1610 dbSNP
rs1242434859 1613 dbSNP
rs1275073345 1616 dbSNP
rs996740705 1624 dbSNP
rs1028690623 1639 dbSNP
rs978386923 1659 dbSNP
rs927222977 1673 dbSNP
rs987455852 1676 dbSNP
rs1184871190 1678 dbSNP
rs1368587637 1688 dbSNP
rs937247554 1693 dbSNP
rs1452454478 1694 dbSNP
rs778030036 1695 dbSNP
rs1372424444 1702 dbSNP
rs1386692075 1703 dbSNP
rs1422748710 1714 dbSNP
rs571591019 1719 dbSNP
rs1255126190 1729 dbSNP
rs1196819893 1731 dbSNP
rs917113982 1736 dbSNP
rs1252387993 1739 dbSNP
rs929808866 1744 dbSNP
rs141763996 1748 dbSNP
rs1300962169 1753 dbSNP
rs920741468 1755 dbSNP
rs1305262809 1758 dbSNP
rs1314916217 1758 dbSNP
rs1443909257 1760 dbSNP
rs1395194220 1761 dbSNP
rs888497221 1764 dbSNP
rs150589204 1765 dbSNP
rs371566361 1766 dbSNP
rs926893952 1773 dbSNP
rs900096146 1774 dbSNP
rs938988081 1776 dbSNP
rs1397099916 1782 dbSNP
rs757300873 1783 dbSNP
rs1030307137 1784 dbSNP
rs1459907418 1786 dbSNP
rs778859449 1788 dbSNP
rs570041895 1789 dbSNP
rs564859987 1790 dbSNP
rs1179064761 1791 dbSNP
rs144427519 1792 dbSNP
rs1365169322 1795 dbSNP
rs1472754808 1796 dbSNP
rs1279649499 1800 dbSNP
rs1160329294 1802 dbSNP
rs997120137 1805 dbSNP
rs1028222559 1806 dbSNP
rs1468591006 1808 dbSNP
rs1305037496 1809 dbSNP
rs572407479 1812 dbSNP
rs147793408 1813 dbSNP
rs1008111370 1815 dbSNP
rs746151551 1815 dbSNP
rs536770081 1821 dbSNP
rs1390873995 1825 dbSNP
rs972116407 1830 dbSNP
rs1028194762 1831 dbSNP
rs1453266285 1831 dbSNP
rs1161297576 1837 dbSNP
rs1305038148 1839 dbSNP
rs1257418139 1840 dbSNP
rs1189320637 1844 dbSNP
rs1486957802 1845 dbSNP
rs1261416654 1846 dbSNP
rs1352527659 1848 dbSNP
rs1349420586 1849 dbSNP
rs1261014652 1850 dbSNP
rs1240541198 1852 dbSNP
rs1332090599 1865 dbSNP
rs375188536 1871 dbSNP
rs190095598 1872 dbSNP
rs1296057722 1873 dbSNP
rs1381447144 1876 dbSNP
rs543687141 1882 dbSNP
rs1321098131 1884 dbSNP
rs1456437352 1885 dbSNP
rs1417203827 1887 dbSNP
rs1211980767 1896 dbSNP
rs1034614348 1897 dbSNP
rs1476439142 1908 dbSNP
rs1480301995 1910 dbSNP
rs992415482 1910 dbSNP
rs1447993125 1913 dbSNP
rs778844846 1918 dbSNP
rs1034048254 1933 dbSNP
rs958598394 1934 dbSNP
rs553088302 1936 dbSNP
rs992798242 1937 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
     
Conditions HeLa
Location of target site 3'UTR
Tools used in this research TargetScan , miRTarCLIP , Piranha
Original Description (Extracted from the article) ... HITS-CLIP data was present in Chi_124A_2A8_130_50. RNA binding protein: AGO. Condition:HeLa cell miR-124 + A ...

- Chi SW; Zang JB; Mele A; Darnell RB, 2009, Nature.

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1
miRNA  3' agggcccuugaguagUCAGAGg 5'
                         |||||| 
Target 5' --------gaaacagAGUCUCa 3'
1 - 14
Article - Chi SW; Zang JB; Mele A; Darnell RB
- Nature, 2009
MicroRNAs (miRNAs) have critical roles in the regulation of gene expression; however, as miRNA activity requires base pairing with only 6-8 nucleotides of messenger RNA, predicting target mRNAs is a major challenge. Recently, high-throughput sequencing of RNAs isolated by crosslinking immunoprecipitation (HITS-CLIP) has identified functional protein-RNA interaction sites. Here we use HITS-CLIP to covalently crosslink native argonaute (Ago, also called Eif2c) protein-RNA complexes in mouse brain. This produced two simultaneous data sets-Ago-miRNA and Ago-mRNA binding sites-that were combined with bioinformatic analysis to identify interaction sites between miRNA and target mRNA. We validated genome-wide interaction maps for miR-124, and generated additional maps for the 20 most abundant miRNAs present in P13 mouse brain. Ago HITS-CLIP provides a general platform for exploring the specificity and range of miRNA action in vivo, and identifies precise sequences for targeting clinically relevant miRNA-mRNA interactions.
LinkOut: [PMID: 19536157]
CLIP-seq Support 1 for dataset Chi_124A_2A8_130_50
Method / RBP HITS-CLIP / AGO
Cell line / Condition HeLa / HeLa cell miR-124 + A
Location of target site ENST00000602149.1 | 3UTR | GAAACAGAGUCUCACUCUGUU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 19536157 / Chi_HITSCLIP
CLIP-seq Viewer Link
MiRNA-Target Expression Profile
Dataset Pearson Correlation P-value for Pearson Correlation Spearman Correlation P-value for Spearman Correlation Samples Chart
MiRNA-Target Expression Profile (TCGA)
Tumor Pearson Correlation P-value for Pearson Correlation Spearman Correlation P-value for Spearman Correlation Samples Chart
108 hsa-miR-873-3p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT081178 MIDN midnolin 2 4
MIRT109809 ZFX zinc finger protein, X-linked 2 4
MIRT242383 TMC5 transmembrane channel like 5 2 4
MIRT444003 METRN meteorin, glial cell differentiation regulator 2 4
MIRT444097 SEPHS1 selenophosphate synthetase 1 2 2
MIRT446158 RPL12 ribosomal protein L12 2 2
MIRT446859 SAMD9L sterile alpha motif domain containing 9 like 2 2
MIRT447275 FZD5 frizzled class receptor 5 2 2
MIRT447391 TMPRSS15 transmembrane protease, serine 15 2 2
MIRT448817 FKBP1A FK506 binding protein 1A 2 4
MIRT450582 HIST1H2BG histone cluster 1 H2B family member g 2 2
MIRT451776 USP36 ubiquitin specific peptidase 36 2 2
MIRT457961 ABCC5 ATP binding cassette subfamily C member 5 2 4
MIRT458424 KLHL38 kelch like family member 38 2 4
MIRT461383 SLFN12L schlafen family member 12 like 2 2
MIRT467793 SLC2A14 solute carrier family 2 member 14 2 2
MIRT476517 GABRB1 gamma-aminobutyric acid type A receptor beta1 subunit 2 2
MIRT480290 C7orf73 short transmembrane mitochondrial protein 1 2 4
MIRT482745 HES7 hes family bHLH transcription factor 7 2 10
MIRT483189 HIST1H2AH histone cluster 1 H2A family member h 2 6
MIRT486545 DCTN4 dynactin subunit 4 2 2
MIRT486581 ZNF619 zinc finger protein 619 2 2
MIRT492604 POLR3E RNA polymerase III subunit E 2 2
MIRT494130 DCAF7 DDB1 and CUL4 associated factor 7 2 6
MIRT496023 ZBED3 zinc finger BED-type containing 3 2 2
MIRT497121 NBEAL1 neurobeachin like 1 2 2
MIRT497400 TMEM245 transmembrane protein 245 2 2
MIRT501410 RANBP10 RAN binding protein 10 2 2
MIRT510947 PPTC7 PTC7 protein phosphatase homolog 2 6
MIRT512494 ARID2 AT-rich interaction domain 2 2 2
MIRT512595 ZNF783 zinc finger family member 783 2 2
MIRT512612 CNTN4 contactin 4 2 2
MIRT517808 UGDH UDP-glucose 6-dehydrogenase 2 6
MIRT520686 TMED7 transmembrane p24 trafficking protein 7 2 4
MIRT526179 HEPH hephaestin 2 2
MIRT532568 CSTF1 cleavage stimulation factor subunit 1 2 2
MIRT533979 TADA2A transcriptional adaptor 2A 2 2
MIRT538622 CCSER2 coiled-coil serine rich protein 2 2 4
MIRT539703 EIF3H eukaryotic translation initiation factor 3 subunit H 2 2
MIRT539806 GAPVD1 GTPase activating protein and VPS9 domains 1 2 2
MIRT540422 FAM83F family with sequence similarity 83 member F 2 2
MIRT540506 CXCL10 C-X-C motif chemokine ligand 10 2 2
MIRT540619 F2RL2 coagulation factor II thrombin receptor like 2 2 2
MIRT542423 ZNF331 zinc finger protein 331 2 2
MIRT542454 AKR7A2 aldo-keto reductase family 7 member A2 2 2
MIRT543383 CC2D2A coiled-coil and C2 domain containing 2A 2 2
MIRT544777 CSTF2T cleavage stimulation factor subunit 2 tau variant 2 4
MIRT544923 ERCC4 ERCC excision repair 4, endonuclease catalytic subunit 2 2
MIRT549768 ZNF611 zinc finger protein 611 2 4
MIRT551242 COLEC10 collectin subfamily member 10 2 2
MIRT560474 ENSA endosulfine alpha 2 2
MIRT569738 GPR173 G protein-coupled receptor 173 2 2
MIRT571297 CHCHD4 coiled-coil-helix-coiled-coil-helix domain containing 4 2 2
MIRT572345 CKAP2L cytoskeleton associated protein 2 like 2 2
MIRT573112 ERBB2IP erbb2 interacting protein 2 2
MIRT607744 ANGPT4 angiopoietin 4 2 2
MIRT607903 SPRYD4 SPRY domain containing 4 2 2
MIRT611744 SERPING1 serpin family G member 1 2 4
MIRT615101 BNC2 basonuclin 2 2 2
MIRT619124 CD40LG CD40 ligand 2 2
MIRT625572 ANKRD42 ankyrin repeat domain 42 2 2
MIRT629038 KLLN killin, p53-regulated DNA replication inhibitor 2 2
MIRT633986 SLC35E2 solute carrier family 35 member E2 2 2
MIRT635675 COX18 COX18, cytochrome c oxidase assembly factor 2 4
MIRT637471 DEFB105B defensin beta 105B 2 4
MIRT637503 DEFB105A defensin beta 105A 2 4
MIRT639735 MAP2K2 mitogen-activated protein kinase kinase 2 2 2
MIRT640730 C9orf64 chromosome 9 open reading frame 64 2 2
MIRT645364 C9orf47 chromosome 9 open reading frame 47 2 2
MIRT647938 RNF152 ring finger protein 152 2 2
MIRT649400 SH2D4A SH2 domain containing 4A 2 2
MIRT656860 KIN Kin17 DNA and RNA binding protein 2 2
MIRT663470 POFUT2 protein O-fucosyltransferase 2 2 2
MIRT663507 NKAPL NFKB activating protein like 2 4
MIRT667690 KNSTRN kinetochore localized astrin/SPAG5 binding protein 2 2
MIRT677403 PCNP PEST proteolytic signal containing nuclear protein 2 2
MIRT678682 SCUBE3 signal peptide, CUB domain and EGF like domain containing 3 2 2
MIRT678789 NUPL2 nucleoporin like 2 2 2
MIRT680649 KIAA1456 KIAA1456 2 2
MIRT682450 MTX3 metaxin 3 2 2
MIRT682740 CA6 carbonic anhydrase 6 2 2
MIRT684421 TUFT1 tuftelin 1 2 2
MIRT690535 TRAPPC2 trafficking protein particle complex 2 2 2
MIRT690595 C17orf105 chromosome 17 open reading frame 105 2 2
MIRT690771 PLA2G2C phospholipase A2 group IIC 2 2
MIRT692233 ALDH1B1 aldehyde dehydrogenase 1 family member B1 2 2
MIRT693667 MXRA7 matrix remodeling associated 7 2 2
MIRT695551 CLPB ClpB homolog, mitochondrial AAA ATPase chaperonin 2 2
MIRT695870 C19orf52 translocase of inner mitochondrial membrane 29 2 2
MIRT696214 LYZ lysozyme 2 2
MIRT698368 TMED4 transmembrane p24 trafficking protein 4 2 2
MIRT700795 PHTF2 putative homeodomain transcription factor 2 2 2
MIRT701640 MYLK3 myosin light chain kinase 3 2 2
MIRT702989 HERPUD2 HERPUD family member 2 2 2
MIRT703627 FBXL3 F-box and leucine rich repeat protein 3 2 2
MIRT703783 FAM102B family with sequence similarity 102 member B 2 2
MIRT704293 DDX19B DEAD-box helicase 19B 2 2
MIRT704828 CDC73 cell division cycle 73 2 2
MIRT705014 CAMK2N1 calcium/calmodulin dependent protein kinase II inhibitor 1 2 2
MIRT708480 OLR1 oxidized low density lipoprotein receptor 1 2 2
MIRT710770 PHF7 PHD finger protein 7 2 2
MIRT718918 TRIM66 tripartite motif containing 66 2 2
MIRT720390 ZNF549 zinc finger protein 549 2 2
MIRT720593 TTC39C tetratricopeptide repeat domain 39C 2 2
MIRT723515 SIGLEC8 sialic acid binding Ig like lectin 8 2 2
MIRT724458 PRKX protein kinase, X-linked 2 2
MIRT737267 UMAD1 UBAP1-MVB12-associated (UMA) domain containing 1 3 0
MIRT737356 ZIC2 Zic family member 2 4 0
miRNA-Drug Associations
miRNA Small Melocule FDA CID Detection Method Condition PMID Year Expression Pattern of miRNA
miR-873 Dexamethasone approved 5743 Microarray adrenals and granulosa cells 24205079 2014 down-regulated
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-mir-873 Ceritinib 57379345 NSC776422 approved resistant High Non-Small Cell Lung Cancer cell line (H3122, H2228)
hsa-mir-873 Dabrafenib 44462760 NSC764134 approved sensitive cell line (A375)
hsa-mir-873 Cisplatin 5460033 NSC119875 approved resistant cell line (OE19)
hsa-mir-873 Ceritinib 57379345 NSC776422 approved resistant cell line (H3122)
hsa-mir-873 Decitabine 451668 approved sensitive tissue (esopheageal cancer)
hsa-miR-873-3p Ceritinib 57379345 NSC776422 approved resistant High Non-Small Cell Lung Cancer cell line (H3122, H2228)
hsa-miR-873-3p Cisplatin 5460033 NSC119875 approved resistant High Ovarian Cancer cell line (A2780)
hsa-miR-873-3p Cisplatin 5460033 NSC119875 approved sensitive High Non-Small Cell Lung Cancer cell line (A549)
hsa-miR-873-3p Gefitinib 123631 NSC715055 approved sensitive cell line (HCC827)
hsa-miR-873-3p Gefitinib 123631 NSC715055 approved sensitive cell line (PC9)
hsa-miR-873-3p Osimertinib 71496458 NSC779217 approved sensitive cell line (HCC827)
hsa-miR-873-3p Vemurafenib 42611257 NSC761431 approved sensitive cell line (451Lu)
hsa-miR-873-3p Cisplatin 5460033 NSC119875 approved sensitive cell line (A549)
hsa-miR-873-3p Gefitinib 123631 NSC715055 approved sensitive cell line (HCC827)
hsa-miR-873-3p Cisplatin 5460033 NSC119875 approved sensitive cell line (A549)
hsa-miR-873-3p Gemcitabine 60750 NSC613327 approved sensitive cell line (PANC-1) (1500 ng/ml)
hsa-miR-873-3p Gemcitabine 60750 NSC613327 approved sensitive cell line (PANC-1) (100 ng/ml)
hsa-miR-873-3p Ceritinib 57379345 NSC776422 approved resistant cell line (H3122)

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